You need to distinguish two aspects :
getting on the rear wheel and staying balance on the rear wheel.
Basically, both can't be solved by the same geometry. Either you go for one or for the other, but you can't have both simultaneously.
A high bar will make pulling the front wheel up much easier. Thus, you will have less problem to maintain the left/right balance during the first phase of a manual (I.e. getting to the balance point).
For a really high bunny up, this can become a drawback, cause you have a really short period for jumping/for the extension. In addition, you start from a higher position, more on the back, but for really high bunny up, one shall slightly transfer his/her mass to the front, which is more difficult when starting too far back. One has less vertical amplitude too.
On the rear wheel with a lower bar, your hips are closer to the balance point, they are more above the bottom bracket. That gives a much better control (moment of rotation is smaller, that makes it easier to control)